The one inside is a pvt. tour operator and other outside is a society under the guidelines of Goa tourism. The same is available is in front of Madgaon Rly. station. u need not pay anything extra than what u paid at the counter - Only thing give your destination very clearly.
Trying to find a taxi returning to one of the resorts after dropping their fare at the airport, is one way to get a cheap ride home. This may save you 2-300 rupees, especially if you see a driver you know. Be careful trying to do this at Margao station, the taxi union gets quiet militant.
Remember its cheaper to just walk out the airport gate, always taxis waiting, depends on your budget and bargaining skills, but these taxis are cheaper than the pre paid inside. Airport to Benaulim pre paid 450 rp, outside 350. These are proper taxis, but freelancers.